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Did you use a Wiring Specialties lower (trans) harness by chance? If so, unplug the 2-pin connector on the alternator and see if you still have these issue.
I just went through a somewhat similar issue, where things would stay powered on after turning off the ignition. Figured out the bulb check relay was getting energized which in turn was keeping the accessory relays energized. Your battery light is what's making me think the issue might be the same even though my issue was on a S13.
Root cause ended up being the 2-pin alternator connector having the wires flipped on my WS lower harness. There's a thick and a thin wire, so should be very easy to compare if you happen to have the old harness laying around.
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